def get_current_contacts(G, data):
cs = data['cellStates']
it = iter(cs)
n = len(cs)
cell_type = {}
pos_dict = {}
for it in cs:
cell_type[cs[it].idx] = cs[it].cellType
pos_dict[cs[it].idx] = cs[it].pos[0:2]
modname = data['moduleName']
moduleStr = data['moduleStr']
sim = Simulator(modname, 0.0, moduleStr=moduleStr, saveOutput=False)
sim.loadFromPickle(data)
sim.phys.update_grid() # we assume local cell_centers is current
sim.phys.bin_cells()
sim.phys.cell_sqs = sim.phys.cell_sqs_dev.get() # get updated cell sqs
sim.phys.sort_cells()
sim.phys.sorted_ids_dev.set(
sim.phys.sorted_ids) # push changes to the device
sim.phys.sq_inds_dev.set(sim.phys.sq_inds)
sim.phys.find_contacts(predict=False)
sim.phys.get_cts()
ct_pts = sim.phys.ct_pts #these are the points on the cell surface - they can be transformed into the global coordinate system
ct_tos = sim.phys.ct_tos #this is the list of *some* contacts from each cell (only for lower cell_ids)
ct_dists = sim.phys.ct_dists
cell_cts = sim.phys.cell_n_cts #not really all the contacts of the cell, because the tos are only defined between a cell and ones with lower ids
generate_network(G, n, ct_tos, cell_cts, pos_dict, cell_type)
def loadPickle(self):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
qs, _ = QFileDialog.getOpenFileName(self,
'Load pickle file',
'',
'*.pickle',
options=options)
if qs and self.getOpenCLPlatDev():
filename = str(qs)
print(filename)
data = pickle.load(open(filename, 'rb'))
if isinstance(data, dict):
self.modName = data['moduleName']
self.moduleStr = data['moduleStr']
self.frameNo = data['stepNum']
sim = Simulator(self.modName, \
self.dt, \
moduleStr=self.moduleStr, \
clPlatformNum=self.clPlatformNum, \
clDeviceNum=self.clDeviceNum, \
is_gui=True)
self.loadingFromPickle = True
sim.loadFromPickle(data)
self.setSimulator(sim)
# Note: the pickle loaded contains the stepNum, hence we now
# need to set the GUI frameNo to match
self.frameNo = self.sim.stepNum
if self.run:
self.frameNo += 1
self.updateGL()
else:
print("Pickle is in an unsupported format, sorry")
def loadPickle(self):
qs = QtWidgets.QFileDialog.getOpenFileName(
self, 'Load pickle file', '',
'*.pickle') #kk:changed QtGui to QtWidgets
if qs and self.getOpenCLPlatDev():
filename = str(qs[0]) #kk: changed how to load pickle
with open(filename, "rb") as input_file:
data = cPickle.load(input_file)
if isinstance(data, dict):
self.modName = data['moduleName']
self.moduleStr = data['moduleStr']
self.frameNo = data['stepNum']
sim = Simulator(self.modName, \
self.dt, \
moduleStr=self.moduleStr, \
clPlatformNum=self.clPlatformNum, \
clDeviceNum=self.clDeviceNum, \
is_gui=True)
self.setSimulator(sim)
self.loadingFromPickle = True
self.sim.loadFromPickle(data)
# Note: the pickle loaded contains the stepNum, hence we now
# need to set the GUI frameNo to match
self.frameNo = self.sim.stepNum
if self.run:
self.frameNo += 1
self.updateGL()
else:
print "Pickle is in an unsupported format, sorry"
def simulate(modfilename, platform, device, steps=50):
(path,name) = os.path.split(modfilename)
modname = str(name).split('.')[0]
sys.path.append(path)
sim = Simulator(modname, 0.25, clPlatformNum=platform, clDeviceNum=device)
while len(sim.cellStates) < max_cells-cell_buffer:
sim.step()
def reset(self):
# Note: we don't ask user to choose OpenCL platform/device on reset, only load
if not self.loadingFromPickle:
reload(self.sim.module)
if self.loadingFromPickle:
sim = Simulator(self.modName, \
self.dt, \
moduleStr=self.moduleStr, \
clPlatformNum=self.clPlatformNum, \
clDeviceNum=self.clDeviceNum)
self.setSimulator(sim)
else:
sim = Simulator(self.modName, \
self.dt, \
clPlatformNum=self.clPlatformNum, \
clDeviceNum=self.clDeviceNum)
self.setSimulator(sim)
self.frameNo = 0
self.updateGL()
def loadModelFile(self, modname):
if self.getOpenCLPlatDev():
self.loadingFromPickle=False
(path,name) = os.path.split(modname)
self.modName = str(name).split('.')[0]
sys.path.append(path)
sim = Simulator(self.modName, \
self.dt, \
clPlatformNum=self.clPlatformNum, \
clDeviceNum=self.clDeviceNum)
self.setSimulator(sim)
self.updateGL()
def simulate(mod_name, steps=50):
print('simulate')
sim = Simulator(mod_name,
0.25,
None,
pickleSteps=50,
pickleFileRoot=pickleFileRoot)
print('start')
sim.phys.set_cells()
sim.phys.calc_cell_geom()
while len(sim.cellStates) < max_cells - cell_buffer:
sim.step()
def simulate(mod_name, config_file):
sim = Simulator(mod_name, 0.25, config_file)
while len(sim.cellStates) < max_cells:
sim.step()
def simulate(mod_name, ingam, fname):
sim = Simulator(mod_name, 0.25, ingam, 25, fname)
while len(sim.cellStates) < max_cells-cell_buffer:
sim.step()
def simulate(mod_name, steps, dt):
sim = Simulator(mod_name, dt)
for i in range(num_steps):
sim.step()
def simulate(mod_name, device):
sim = Simulator(mod_name, 0.25, device)
while len(sim.cellStates) < max_cells-cell_buffer:
sim.step()
